ArticleInternational journal of molecular sciences2019
Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Implementation of Nonisobaric TMT Analogs for Accurate Precursor-Level Quantification by plexDIA.Rapid communications in mass spectrometry : RCM · 2026Article
- Monoallelic mutations in MMD2 cause autosomal dominant aggressive periodontitis.The Journal of experimental medicine · 2025Article
- Proteome profile differences among human, monkey, and mouse brain microvessels and cultured brain microvascular endothelial cells.Fluids and barriers of the CNS · 2025Article
- Quantitative proteomic analysis based on TMT reveals different responses of Haloxylon ammodendron and Haloxylon persicum to long-term drought.BMC plant biology · 2025Article
- Screening of functional genes affecting the quality of translucent eggshell membranes based on RNA-seq analysis and DIA proteomics.Frontiers in veterinary science · 2025Article
- Multi-omics approach to dissect the significance of lipid metabolism in helper T cell subset.Frontiers in immunology · 2025Review
- Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics.International journal of molecular sciences · 2024Article
- Advances in omics data for eosinophilic esophagitis: moving towards multi-omics analyses.Journal of gastroenterology · 2024Review
- A Non-targeted Proteomics Newborn Screening Platform for Inborn Errors of Immunity.Journal of clinical immunology · 2024Article
- Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation.International journal of molecular sciences · 2024Article
- Organelle communication maintains mitochondrial and endosomal homeostasis during podocyte lipotoxicity.JCI insight · 2024Article
- Host-derived protein profiles of human neonatal meconium across gestational ages.Nature communications · 2024Article
- Article
- Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity.iScience · 2024Article
- L-type amino acid transporter 1 inhibitor JPH203 prevents the growth of cabazitaxel-resistant prostate cancer by inhibiting cyclin-dependent kinase activity.Cancer science · 2024Article
- Perifascial areolar tissue graft promotes angiogenesis and wound healing in an exposed ischemic component rabbit model.PloS one · 2024Article
- Inflammatory profile of eosinophils in asthma-COPD overlap and eosinophilic COPD: a multi-omics study.Frontiers in immunology · 2024Article
- Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry.Biology methods & protocols · 2024Article
- Application of machine learning for mass spectrometry-based multi-omics in thyroid diseases.Frontiers in molecular biosciences · 2024Review
- CD39+CD55- Fb Subset Exhibits Myofibroblast-Like Phenotype and Is Associated with Pain in Osteoarthritis of the Knee.Biomedicines · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteomic analysis overtop the existing data-dependent acquisition (DDA)-MS-based proteomic analysis to enable deep proteome coverage and precise relative quantitative analysis in single-shot liquid chromatography (LC)-MS/MS. However, DIA-MS-based proteomic analysis has not yet been optimized in terms of system robustness and throughput, particularly for its practical applications. We established a single-shot LC-MS/MS system with an MS measurement time of 90 min for a highly sensitive and deep proteomic analysis by optimizing the conditions of DIA and nanoLC. We identified 7020 and 4068 proteins from 200 ng and 10 ng, respectively, of tryptic floating human embryonic kidney cells 293 (HEK293F) cell digest by performing the constructed LC-MS method with a protein sequence database search. The numbers of identified proteins from 200 ng and 10 ng of tryptic HEK293F increased to 8509 and 5706, respectively, by searching the chromatogram library created by gas-phase fractionated DIA. Moreover, DIA protein quantification was highly reproducible, with median coefficients of variation of 4.3% in eight replicate analyses. We could demonstrate the power of this system by applying the proteomic analysis to detect subtle changes in protein profiles between cerebrums in germ-free and specific pathogen-free mice, which successfully showed that >40 proteins were differentially produced between the cerebrums in the presence or absence of bacteria.
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